2XD6

Hsp90 complexed with a resorcylic acid macrolactone.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Inhibition of Hsp90 with Resorcylic Acid Macrolactones. Synthesis and Binding Studies.

Day, J.E.H.Sharp, S.Y.Rowlands, M.G.Aherne, W.Lewis, W.Roe, S.M.Prodromou, C.Pearl, L.H.Workman, P.Moody, C.J.

(2010) Chemistry 16: 10366

  • DOI: 10.1002/chem.201001119
  • Primary Citation of Related Structures:  
    2XD6

  • PubMed Abstract: 
  • A series of resorcylic acid macrolactones, analogues of the natural product radicicol has been prepared by chemical synthesis, and evaluated as inhibitors of heat shock protein 90 (Hsp90), an emerging attractive target for novel cancer therapeutic agents ...

    A series of resorcylic acid macrolactones, analogues of the natural product radicicol has been prepared by chemical synthesis, and evaluated as inhibitors of heat shock protein 90 (Hsp90), an emerging attractive target for novel cancer therapeutic agents. The synthesis involves acylation of an ortho-toluic acid dianion, esterification, followed by a ring-closing metathesis to form the macrocycle. Subsequent manipulation of the protected hydroxymethyl side chain allows access to a range of new analogues following deprotection of the two phenolic groups. Co-crystallization of one of the new macrolactones with the N-terminal domain of yeast Hsp90 confirms that it binds in a similar way to the natural product radicicol and to our previous synthetic analogues, but that the introduction of the additional hydroxymethyl substituent appears to result in an unexpected change in conformation of the macrocyclic ring. As a result of this conformational change, the compounds bound less favorably to Hsp90.


    Organizational Affiliation

    School of Chemistry, University of Nottingham, University Park, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-DEPENDENT MOLECULAR CHAPERONE HSP82A214Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P02829 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02829 
Go to UniProtKB:  P02829
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02829
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XD6
Query on XD6

Download Ideal Coordinates CCD File 
B [auth A](5Z)-13-CHLORO-14,16-DIHYDROXY-1,11-DIOXO-3,4,7,8,9,10,11,12-OCTAHYDRO-1H-2-BENZOXACYCLOTETRADECINE-6-CARBALDEHYDE
C18 H19 Cl O6
XRPZFFJMSSNWNE-WZUFQYTHSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
XD6 Binding MOAD:  2XD6 IC50: 650 (nM) from 1 assay(s)
PDBBind:  2XD6 IC50: 650 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.767α = 90
b = 73.767β = 90
c = 110.284γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SAINTdata reduction
XPREPdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-12-28
    Changes: Database references
  • Version 1.2: 2013-05-01
    Changes: Non-polymer description, Refinement description, Version format compliance
  • Version 1.3: 2017-07-05
    Changes: Data collection